# Output of GENECONV for sequence file SCNA_amphibian_CDS_alignment_PAL2NAL.fasta # GENECONV version 1.81 # Command line: GENECONV SCNA_amphibian_CDS_alignment_PAL2NAL.fasta # amphibian_group_7.cfg /g1 # Contents of parameter configuration file: # amphibian_group_7.cfg: -Startseed=123 # -group Ambystoma SCN1A_Ambystoma_mexicanum # SCN2A_Ambystoma_mexicanum SCN3A_Ambystoma_mexicanum # -group Pleurodeles SCN1A_Pleurodeles_waltl SCN2A_Pleurodeles_waltl # SCN3A_Pleurodeles_waltl # -group Notophthalmus SCN1A_Notophthalmus_viridescens # SCN2A_Notophthalmus_viridescens SCN3A_Notophthalmus_viridescens # -group Tgranulosa SCN1A_Taricha_granulosa SCN2A_Taricha_granulosa # SCN3A_Taricha_granulosa # -group Ttorosa SCN1A_Taricha_torosa SCN2A_Taricha_torosa # SCN3A_Taricha_torosa # -group Crypto SCN1A_Cryptobranchus_alleganiensis # SCN2A_Cryptobranchus_alleganiensis SCN3A_Cryptobranchus_alleganiensis # -group Plethodon SCN1A_Plethodon_cinereus SCN2A_Plethodon_cinereus # SCN3A_Plethodon_cinereus # # SCNA_amphibian_CDS_alignment_PAL2NAL.fasta: 42 sequences. # # Options and features: Using 21 DNA sequences, 6345 aligned bases, # 1826 polymorphisms, FASTA format, gscale=1 for mismatches, # 7 groups defined, maxSimPairPval=0.05, maxSimGlobPval=0.05, # no maxKAPairPval limits, no maxKAGlobPval limits, # simPvals based on 10,000 permutations, # global P-values based on BLAST-like global scores, # fragment limits: minlength=1, minnpolys=2, minscore=2, # no pairwise fragment lists, at most one overlapping fragment, # starting seed=123, contiguous sites with indels are one polymorphism, # 25 indel blocks with up to 396 sites each, # no match (replacement) char in source file. # Groups: # Ambystoma (3): SCN1A_Ambystoma_mexicanum SCN2A_Ambystoma_mexicanum # SCN3A_Ambystoma_mexicanum # Pleurodeles (3): SCN1A_Pleurodeles_waltl SCN2A_Pleurodeles_waltl # SCN3A_Pleurodeles_waltl # Notophthalmus (3): SCN1A_Notophthalmus_viridescens # SCN2A_Notophthalmus_viridescens SCN3A_Notophthalmus_viridescens # Tgranulosa (3): SCN1A_Taricha_granulosa SCN2A_Taricha_granulosa # SCN3A_Taricha_granulosa # Ttorosa (3): SCN1A_Taricha_torosa SCN2A_Taricha_torosa # SCN3A_Taricha_torosa # Crypto (3): SCN1A_Cryptobranchus_alleganiensis # SCN2A_Cryptobranchus_alleganiensis # SCN3A_Cryptobranchus_alleganiensis # Plethodon (3): SCN1A_Plethodon_cinereus SCN2A_Plethodon_cinereus # SCN3A_Plethodon_cinereus # Sequences not in group list: SCN8A_Ambystoma_mexicanum # SCN8A_Notophthalmus_viridescens SCN8A_Taricha_granulosa # SCN8A_Taricha_torosa SCN8A_Pleurodeles_waltl # SCN8A_Cryptobranchus_alleganiensis SCN8A_Plethodon_cinereus # SCN4A_Ambystoma_mexicanum SCN4A_Pleurodeles_waltl # SCN4A_Notophthalmus_viridescens SCN4A_Taricha_granulosa # SCN4A_Taricha_torosa SCN4A_Cryptobranchus_alleganiensis # SCN4A_Plethodon_cinereus SCN5A_Ambystoma_mexicanum # SCN5A_Notophthalmus_viridescens SCN5A_Taricha_granulosa # SCN5A_Taricha_torosa SCN5A_Pleurodeles_waltl # SCN5A_Plethodon_cinereus SCN5A_Cryptobranchus_alleganiensis # Looking at within-group fragments only (7 groups) # # Mismatch penalty: 1 * npolys / num_ppen # where `num_ppen' is the number of ``potential penalties'': # sequence differences for inner fragments, # local monomorphisms for outer fragments. # Nucleotide codes in data: T(33,912) C(24,934) A(36,354) G(27,854) # Other(10,191) CG/TCAG ratio: 42.90% # Non-nucleotide characters in data: -(2DH)(n=10,086) N(4EH)(n=105) # 2347 sites with missing data or unrecognized characters. # (These characters are treated as indels for the # purpose of creating indel blocks.) # 247 sites with all gap or unrecognized characters. # 1799 polymorphic and 2199 monomorphic sites with no indels. # 2 single polymorphic sites with indels. # 25 indel blocks with more than one site # (each block is treated as a single polymorphism). # 1826 polymorphisms to be permuted. # # The starting random number seed is 123. # Simulated P-values are based on 10,000 permutations. # Maximum BLAST-like scores (21 sequences, 7 groups): # Inner Max Sim S.D.s above S.D. of # frags Score P-value sim. mean sims # SCORE 45.866 0.0000 34.51 1.2413 # OuterSeq # frags 14.968 0.0000 9.52 1.2840 # # Global lists: 20 I and 5 O significant fragments # Pairwise lists: No fragments listed # where I means inner pair, O is outer seq, A is outer pair, and # G means outer group (fragments). # Global P-values are based on BLAST-like global scores. # # Fragment offsets and lengths are in nucleotides. # Note: A polymorphism can be at a run of sites with indels, # which here have up to 396 sites. # Bases other than `TCAGU' are treated as indels # for the purpose of generating polymorphisms. # # # Global inner fragments (1826 polymorphisms, 6345 aligned bases): # (Inner fragments are runs of matching sites with penalties.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 21. # Num Poly is the number of polymorphic sites in the fragment. # Num Dif is the number of mismatches within the fragment. # Tot Difs is the total number of mismatches between two sequences. # MisM Pen is the penalty per mismatch for these two sequences. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Names Pvalue Pvalue Begin End Len Poly Dif Difs Pen. GI SCN1A_Plethodon_cinereus;SCN2A_Plethodon_cinereus 0.0000 0.00000 4231 4754 524 138 9 838 3 GI SCN2A_Ambystoma_mexicanum;SCN3A_Ambystoma_mexicanum 0.0000 0.00000 619 1244 626 74 2 902 3 GI SCN1A_Cryptobranchus_alleganiensis;SCN2A_Cryptobranchus_alleganiensis 0.0003 0.00040 5428 5798 371 177 27 621 3 GI SCN1A_Plethodon_cinereus;SCN3A_Plethodon_cinereus 0.0005 0.00094 1110 1685 576 88 13 786 3 GI SCN1A_Plethodon_cinereus;SCN3A_Plethodon_cinereus 0.0005 0.00094 2566 2742 177 68 8 786 3 GI SCN1A_Plethodon_cinereus;SCN2A_Plethodon_cinereus 0.0005 0.00128 31 94 64 31 0 838 3 GI SCN1A_Ambystoma_mexicanum;SCN2A_Ambystoma_mexicanum 0.0008 0.00165 4003 4409 407 134 25 794 3 GI SCN1A_Cryptobranchus_alleganiensis;SCN2A_Cryptobranchus_alleganiensis 0.0011 0.00243 4157 4532 376 153 23 621 3 GI SCN1A_Notophthalmus_viridescens;SCN3A_Notophthalmus_viridescens 0.0033 0.00587 2008 2096 89 41 1 733 3 GI SCN1A_Notophthalmus_viridescens;SCN2A_Notophthalmus_viridescens 0.0067 0.01472 4136 4427 292 109 20 796 3 GI SCN1A_Ambystoma_mexicanum;SCN2A_Ambystoma_mexicanum 0.0106 0.02472 31 123 93 48 5 794 3 GI SCN1A_Ambystoma_mexicanum;SCN3A_Ambystoma_mexicanum 0.0117 0.02733 139 266 128 54 5 722 3 GI SCN1A_Taricha_granulosa;SCN3A_Taricha_granulosa 0.0145 0.03500 1147 1251 105 41 2 725 3 GI SCN1A_Taricha_torosa;SCN3A_Taricha_torosa 0.0145 0.03500 1147 1251 105 41 2 725 3 GI SCN1A_Ambystoma_mexicanum;SCN2A_Ambystoma_mexicanum 0.0171 0.03882 4449 4532 84 35 2 794 3 GI SCN1A_Ambystoma_mexicanum;SCN3A_Ambystoma_mexicanum 0.0175 0.03909 4136 4262 127 37 1 722 3 GI SCN2A_Cryptobranchus_alleganiensis;SCN3A_Cryptobranchus_alleganiensis 0.0180 0.04301 5269 5674 406 164 32 693 3 GI SCN2A_Plethodon_cinereus;SCN3A_Plethodon_cinereus 0.0218 0.04919 2458 2540 83 29 2 897 3 GI SCN1A_Pleurodeles_waltl;SCN3A_Pleurodeles_waltl 0.0303 0.06728 4942 4997 56 30 0 738 3 GI SCN1A_Plethodon_cinereus;SCN3A_Plethodon_cinereus 0.0343 0.07706 5125 5258 134 46 5 786 3 # # 20 inner fragments listed. # 16,602 overlapping fragments discarded. # # # Global outer-sequence fragments (1826 polymorphisms, 6345 aligned bases): # (Outer-sequence fragments are runs of sites that are unique in that group.) # (Sim and BC KA P-values are corrected for multiple comparisons.) # (Fragments are listed only if Sim P-value <= 0.05.) # See earlier in the file for the full restrictions on fragments. # # BC KA means Bonferroni-corrected KA (BLAST-like) Pvalues. # KA Pvalues are NOT corrected for multiple pairwise comparisons. # In the following table, BC Pvalues are KA Pvalues multiplied by 21. # Num Poly is the number of polymorphic sites in the fragment. # Num Mat is the number of nonunique sites within the fragment. # Tot Mats is the total number of nonunique sites for that sequence. # MisM Pen is the penalty per nonunique site for this sequence. # # Seq Sim BC KA Aligned Offsets Num Num Tot MisM # Name Pvalue Pvalue Begin End Len Poly Mat Mats Pen. GO SCN2A_Ambystoma_mexicanum 0.0000 0.00001 5728 6201 474 59 13 1260 2 GO SCN2A_Cryptobranchus_alleganiensis 0.0096 0.01774 2026 2042 17 10 0 1403 2 GO SCN3A_Plethodon_cinereus 0.0152 0.03473 4398 4412 15 14 1 1318 2 GO SCN3A_Cryptobranchus_alleganiensis 0.0395 0.08972 4435 4443 9 8 0 1462 2 GO SCN3A_Plethodon_cinereus 0.0482 0.11664 3793 3815 23 13 1 1318 2 # # 5 outer-sequence fragments listed. # 1250 overlapping fragments discarded. # # # No pairwise fragment lists. # (See earlier in the file for the restrictions on fragments.) #